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AmberTools

Category: Science Apps-Molecular Dynamics

Description

AmberTools is a set of programs for biomolecular simulation and analysis. They are designed
to work well with each other, and with the regular Amber suite of programs. You can perform
many simulation tasks with AmberTools, and you can do more extensive simulations with the
combination of AmberTools and Amber itself.

Amber is the collective name for a suite of programs that allow users to carry out molecular
dynamics simulations, particularly on biomolecules. None of the individual programs carries
this name, but the various parts work reasonably well together, and provide a powerful framework
for many common calculations. The term amber is also sometimes used to refer to
the empirical force fields that are implemented here. It should be recognized however,
that the code and force field are separate: several other computer packages have implemented
the amber force fields, and other force fields can be implemented with the Amber programs.
Further, the force fields are in the public domain, whereas the codes are distributed under a
license agreement.

The Amber software suite is now divided into two parts: AmberTools, a collection of freely
available programs mostly under the GPL license, and Amber, which is centered around the
sander and pmemd simulation programs, and which continues to be licensed as before, under a
more restrictive license.

Use

Access to the AmberTools package is provided through the ambertools module. This module sets up environmental variables and the required paths. All binaries except for ptraj.MPI can be run on service nodes. These may be used on login nodes and within batch scripts. The ptraj.MPI executable must be run on the compute nodes via mpirun.

module load ambertools
qsub [PBS Script]

Within the PBS script, all binaries except ptraj.MPI can be run as usual. The ptraj.MPI binary must be run on the compute nodes via mpirun.
mpirun -np [number of cores] -N [cores per node] ptraj.MPI [program options]